@Article{BIOC,
  author = {Robert C Gentleman and Vincent
J. Carey and Douglas M. Bates and 
Ben Bolstad and Marcel
Dettling and Sandrine Dudoit and Byron Ellis and
Laurent Gautier
and Yongchao Ge and Jeff Gentry and Kurt Hornik and 
Torsten
Hothorn and Wolfgang Huber and Stefano Iacus and  Rafael
Irizarry
and Friedrich Leisch and Cheng Li and Martin Maechler and Anthony J. Rossini
and Gunther Sawitzki and Colin Smith and Gordon Smyth and Luke Tierney
and Jean Y. H. Yang and  Jianhua Zhang},
  title = {Bioconductor: Open software development for 
computational biology and bioinformatics},
  journal = {Genome Biology},
  volume = {5},
  year = {2004},
  pages = {R80},
}


@article{Appay,
	author  = {Appay, V and van Lier, R A W and Sallusto, F and Roederer, M}, 
	title   = {Phenotype and Function of Human T Lymphocyte Subsets: Consensus and Issues},
	journal = {Cytometry A}, 
	year  = {2008},
		  volume= {73A}, 
	 	  pages = {975-983},
}		


@ARTICLE{Maecker2005,
  author =	 {Holden T Maecker and Aline Rinfret and Patricia
                  D'Souza and Janice Darden and Eva Roig and Claire
                  Landry and Peter Hayes and Josephine Birungi and Omu
                  Anzala and Miguel Garcia and Alexandre Harari and
                  Ian Frank and Ruth Baydo and Megan Baker and
                  Jennifer Holbrook and Janet Ottinger and Laurie
                  Lamoreaux and C. Lorrie Epling and Elizabeth
                  Sinclair and Maria A Suni and Kara Punt and Sandra
                  Calarota and Sophia El-Bahi and Gailet Alter and
                  Hazel Maila and Ellen Kuta and Josephine Cox and
                  Clive Gray and Marcus Altfeld and Nolwenn Nougarede
                  and Jean Boyer and Lynda Tussey and Timothy Tobery
                  and Barry Bredt and Mario Roederer and Richard Koup
                  and Vernon C Maino and Kent Weinhold and Giuseppe
                  Pantaleo and Jill Gilmour and Helen Horton and
                  Rafick P Sekaly},
  title =	 {Standardization of cytokine flow cytometry assays.},
  journal =	 {BMC Immunol},
  year =	 {2005},
  volume =	 {6},
  pages =	 {13},
}

@Manual{Rmain,
  title =	 {R: A Language and Environment for Statistical
                  Computing},
  author =	 {{R Development Core Team}},
  organization = {R Foundation for Statistical Computing},
  address =	 {Vienna, Austria},
  year =	 2008,
}

@misc{Rweb,
  url =		 {http://www.r-project.org},
  year =	 2008
}

@article{SpidlenInPressCytometryA,
  title =	 {Gating-ML: XML-based Gating Descriptions in Flow
                  Cytometry.},
  author =	 {Spidlen, J. and Leif, R.C. and Moore, W. and 
                  Roederer, M. and International Society for the Advancement
                  of Cytometry Data Standards Task Force and Brinkman, R.R.},
  journal =	 {Cytometry A},
  volume =	 {73A},
  number =	 {12},
  pages =	 {1151--1157},
  year =	 {2008}
}

@misc{biocweb,
  url =		 {http://www.bioconductor.org},
  year =	 2008
}

@article{brinkman2007hcf,
  title =	 {{High-Content Flow Cytometry and Temporal Data
                  Analysis for Defining a Cellular Signature of
                  Graft-Versus-Host Disease}},
  author =	 {Brinkman, R.R. and Gasparetto, M. and Lee,
                  S.J.J. and Ribickas, A.J. and Perkins, J. and
                  Janssen, W. and Smiley, R. and Smith, C.},
  journal =	 {Biology of Blood and Marrow Transplantation},
  volume =	 {13},
  number =	 {6},
  pages =	 {691--700},
  year =	 {2007},
  publisher =	 {Elsevier}
}

@misc{flowcoreweb,
  url =
                  {http://bioconductor.org/packages/2.2/bioc/html/flowCore.html},
  year =	 2008
}

@article{gasparetto2004ice,
  title =	 {{Identification of compounds that enhance the
                  anti-lymphoma activity of rituximab using flow
                  cytometric high-content screening}},
  author =	 {Gasparetto, M. and Gentry, T. and Sebti, S. and
                  O'Bryan, E. and Nimmanapalli, R. and Blaskovich,
                  M.A. and Bhalla, K. and Rizzieri, D. and Haaland,
                  P. and Dunne, J. and others},
  journal =	 {Journal of Immunological Methods},
  volume =	 292,
  number =	 {1-2},
  pages =	 {59--71},
  year =	 {2004},
  publisher =	 {Elsevier}
}

@article{gentleman2006bos,
  title =	 {{Bioconductor: open software development for
                  computational biology and bioinformatics}},
  author =	 {Gentleman, R.C. and Carey, V.J. and Bates, D.M. and
                  Bolstad, B. and Dettling, M. and Dudoit, S. and
                  Ellis, B. and Gautier, L. and Ge, Y. and Gentry,
                  J. and others},
  journal =	 {feedback},
  year =	 2006
}

@book{lattice,
  author =	 {Deepayan Sarkar},
  title =	 {Lattice: Multivariate Data Visualization With R},
  publisher =	 {Springer},
  year =	 2008
}

@article{lizard2007fca,
  title =	 {{Flow cytometry analyses and bioinformatics:
                  interest in new softwares to optimize novel
                  technologies and to favor the emergence of
                  innovative concepts in cell research.}},
  author =	 {Lizard, G.},
  journal =	 {Cytometry A},
  volume =	 71,
  number =	 9,
  pages =	 {646--647},
  year =	 2007
}

@article{lo2008agf,
  title =	 {{Automated gating of flow cytometry data via robust
                  model-based clustering.}},
  author =	 {Lo, K. and Brinkman, RR and Gottardo, R.},
  journal =	 {Cytometry A},
  volume = 73,
  number = 4,
  pages = {321--332},
  year =	 2008
}

@article{sarkar2008ufv,
  title =	 {{Using flowViz to visualize flow cytometry data}},
  author =	 {Sarkar, D. and Le Meur, N. and Gentleman, R.},
  journal =	 {Bioinformatics},
  volume =	 24,
  number =	 6,
  pages =	 {878--879},
  year =	 2008,
  publisher =	 {Oxford Univ Press}
}

@article{seamer1997pnd,
  title =	 {{Proposed new data file standard for flow cytometry,
                  version FCS 3. 0}},
  author =	 {Seamer, LC and Bagwell, CB and Barden, L. and
                  Redelman, D. and Salzman, GC and Wood, JCS and
                  Murphy, RF},
  journal =	 {Cytometry},
  volume =	 28,
  number =	 2,
  pages =	 {118--122},
  year =	 1997
}

@article{wand2008,
  title =	 {{Feature Significance for Multivariate Kernel
                  Density Estimation.}},
  author =	 {Duong, T. and Cowling, A. and Koch, I. and Wand,
                  M.P.},
  journal =	 {Computational Statistics and Data Analysis},
  volume =	 52,
  number =	 9,
  pages =	 {4225-4242},
  year =	 2008,
  publisher =	 {Elsevier}
}

@article{wand2008_2,
  title =	 {{Highest Density Difference Region Estimation with
                  Application to Flow Cytometric Data.}},
  author =	 {Duong, T. and Cowling, A. and Koch, I. and Wand,
                  M.P.},
  journal =	 {under review},
  year =	 2008
}


@article{mahnke2007omi,
  title={{Optimizing a Multicolor Immunophenotyping Assay}},
  author={Mahnke, Y.D. and Roederer, M.},
  journal={Clinics in Laboratory Medicine},
  volume={27},
  number={3},
  pages={469--485},
  year={2007},
  publisher={Elsevier}
}

@article{Parks:2006,
author = {David R Parks and Mario Roederer and Wayne A Moore}, 
journal = {Cytometry A},
title = {A new "Logicle" display method avoids deceptive effects of logarithmic scaling for low signals and compensated data},
number = {6},
pages = {541--551},
volume = {69},
year = 2006
}
